Pikmin: The Lost Days
by Kage23
Summary: After Captain Olimar rebuilds the Dolphin and leaves, weird things start happening. New, powerful enemies show up, the areas change and transform, and strange chasms open up in the ground. What will happen to the Pikmin, and how will they handle it? Rated T for violence
1. Chapter 1: Remembering

_I was thrown through the air and I landed right in front of the giant beast. The titanic Emperor Bulblax walked lazily over to me, drooling at the sight of us. We could become its meal for the day, but we had other ideas. It prepared to stick its tongue out, but I launched the bomb-rock I was carrying at the Bulblax, which stunned the monster. I was called back by the Captain, who moved the group towards the Bulblax's face._

 _One by one the Captain launched our red brethren onto its face. Its face twisted in agony as the Red Pikmin started to attack it, its face being swatted hundreds of times. This was it... this was our final battle. Everyone could sense it – I, my brethren, and the Captain. We were all tense because the Captain could make one false throw and we'd be all dead._

 _The beast started to recover. The Captain called the Pikmin back, but as soon as he did, the Bulblax jumped high into the air. The Captain saw it jump, and we quickly retreated to the edge of the sandy arena. The Bulblax came back down with a deafening crash, and then it saw how far away our group was. Uninterested, the beast turned around. This was our chance to attack._

 _The Captain threw a few bomb-rock-carrying Yellow Pikmin near the Bulblax, which captured its attention. It again slowly walked towards them and tried to lick them up, but they threw their bomb-rocks at the beast, and once more was it stunned. We rushed in again to attack. It was in more of a daze than last time, since it ate more bomb-rocks this time. It was struggling now. Still a ways from death, but it was definitely struggling.  
_

 _However, we overestimated the power of the bomb-rocks: the Bulblax suddenly hopped and shook off all the Pikmin that were on it. This caught the Captain by surprise, who tried to reassemble our group before the Bulblax could counterattack. In the middle of the confusion, though, the Bulblax licked up several Pikmin, and I winced when I heard their cries. We hastily returned to the edge of the arena again. Our group was getting smaller..._

 _I noticed a resolute look come across the Captain's face. He seemed determined to defeat the Bulblax and avenge the Pikmin's deaths. We looked at the Bulblax, which was just mindlessly roaming around the arena. The Captain took a deep breath, whistled the remaining bomb-rock carriers and threw them near the Bulblax. The beast turned around and saw the Pikmin, but as soon as it did, the bomb-rocks were thrown at it. The combined explosion of the thirteen bomb-rocks stunned it._

 _This was our chance to finish it off. We once more advanced towards the helpless creature. All of the Red Pikmin were thrown on it, and before I knew it, I was thrown at its face, too. I latched onto its ugly snout and I furiously whacked my stem. We had to defeat it. We had to! We had to do this! We had to do it to save our Captain! And we had to avenge the Pikmin that died!  
_

 _Suddenly, the Bulblax lurched up suddenly, and we were all shaken off. It tried to eat us one last time, but it seemed to start choking. It convulsed violently as it spat out some sort of container. Out of the corner of my eye, the Captain was overjoyed, but I was more fascinated what was happening to the Bulblax. Despite releasing the object, it kept choking, and it released saliva everywhere. Then the sand underneath it seemed to give way, and the Bulblax was sucked into the ground, never to be seen again. Five 5-pellets emerged from the sand. I turned to face the Captain, who was literally jumping for joy. We did it... we killed the Bulblax. I cheered inside my mind, and I'm sure the rest of the Pikmin were too.  
_

 _The Captain ordered us to carry the pellets and the container, which was **very** heavy. I heard tiny things jingling in there as we carried it. No wonder the Captain was so happy __– it was his safe! We eventually returned to the landing site, and the Captain bred 15 more Reds and 10 more Yellows. Sorry, Blues... Then the safe was appraised by the Captain's ship. After it absorbed the safe, it seemed to sparkle, and he again jumped for joy. His ship was complete!  
_

 _Nightfall quickly came, but before it did, the Captain ventured off by himself for a bit and returned with a peculiar round object, which was dirty and bent. Then he walked over to his ship. He looked back at us and moved his hand up and down. Was it some sort of farewell gesture? We turned our heads in confusion, and the Captain lowered his. I got one last look at him before he went into his ship. Its engines activated and it blasted off into the sky, and it quickly disappeared. Our leader was gone._

 _But our courage was not._

 _Now that we had repopulated, we had a chance to survive. We had a chance to turn everything around and come back. I felt inspiration rising up in me. I saw a Red Bulborb nearby, and I rushed over to it. The other Pikmin joined me and we took it down by ourselves. I felt a sense of accomplishment and happiness._

 _But if we are going to make a comeback, how would we do it? And what's going to happen to us now? Ugh... too many questions, too many unknowns. We would figure stuff out later and do things one at a time. We carried back the Red Bulborb to the Blue Onion, plucked them, and then we lifted off. The hum of the Onion soothed me as I fell asleep. Today was a very long day..._

* * *

 **DISCLAIMER: Pikmin and related elements are owned by Nintendo.  
**

 **Author's Note: Well, I hope I described the ending to Pikmin 1 okay. I've always wondered what happens to the Pikmin in between the first two games, since so much changes... that made me want to write about it. So here we are! Ugh... When I post this, I'll have... 2 stories. Yay. I really should write more, but lazy. :P So what do you think so far? Please review! Don't be afraid to criticize. (I'm always self-criticizing my writing because I think they have too many big words... but I'll let you guys decide that.) Oh, and thanks for reading!**

 **-PikFan23**


	2. Chapter 2: Discovery

That all happened about a week ago.

And since then, things have been quite different.

First off, the Captain is gone. The first day after he left – well, the first _night_ , I should say, after we had taken off – the grief just hit us really hard as we realized the Captain had left. The grief was so overwhelming that we didn't even land for three days. Then we started to accept his departure, but our sadness turned into boredom. On the fourth morning after he left, wanted to land somewhere. The thing is, when he was here, our Onions would follow him, no matter which area he decided to go to. But since he's gone, we all didn't know where we should land. That same morning, we were tossing around ideas, but we kept disagreeing with each other, and it turned into a big argument. So ever since the fourth morning after his departure, we've been arguing and bickering over which area we should land in. But that isn't the only thing that's changed.

When we land in an area, we have no idea what to do, since we've already done everything we need to do. At least, we _think_ we've done everything... So we pretty much kill the monsters in the area and increase our population. Oh, another thing: for whatever reason, the Onions wouldn't let out more than 100 Pikmin at a time when the Captain was here. Now the Onions let out unlimited Pikmin, so Pikmin aren't born inside the Onions anymore. When we finish increasing our population, we explore the area, looking for things to do. Since I'm a Yellow, my friends (who are also Yellows) and I like to play with the bomb rocks scattered around the area. We've been thinking about sneaking up on the others and scaring them with an explosion...but we don't want to accidentally kill someone or we'd feel terrible about it. The truth is, I have scared other Pikmin before, and now I have a habit of scaring them a lot. Because of that, my name is Shock.

Anyway, today we decide to land in the Forest of Hope. We've cleared the area of all the enemies... Except for the Burrowing Snagrets. We have a score to settle with those awful Burrowing Snagrets, and if we defeat them, they'd be a huge boost to our population. The Onions fly south towards the Forest of Hope. I watch through the window as we descend beneath the leafy, eternal canopy of the trees. The descent always amazes me, because one moment we're in the open sky, so wide and vast, and then the next moment, we're down in the forest, which is dark and hidden away from the world... The Onion's landing startles me out of my thoughts. I rush to exit with the other Yellows. We climb out of the Onion and join up with the other Pikmin types, and we begin to discuss how we should go about attacking the Snagrets. I know that at some point it'll just turn into an argument, like discussions always do, and I don't want to be there for that. I decide to leave, and I motion some of my friends to sneak off with me. We start walking over to the place where the Nova Blaster was at, since there are bomb rocks there.

As we reach the bomb rocks, I notice a weird plant nearby. I don't recognize it, and I get the others to look at it.

"What's that?" says Stacy, one of my friends. Stacy has a rare immunity to electricity, something that is revered among Yellow Pikmin, so she is pretty well respected among the Yellows. (That's also where her name comes from. Get it, static, Stacy...?)

"Is that a new plant?" says Blast, another one of my friends. He's just a regular Yellow Pikmin, though he _loves_ bomb rocks. But I mean, what Yellow doesn't love bomb rocks? They're so _fun._

"I don't think that was there before," I say. "Let's go look at it!" I throw Stacy and Blast onto the ledge above us, since there's no geyser, and they pull me up. We're now on the place where the Shock Absorber once was. The plant is a little taller than the Pellet Posies, but it looks like it's trying to grow.

"It must've sprouted recently," says Stacy. "It looks like it's pretty young."

Just as she says that, the plant suddenly grows in size. It's now twice as tall as the Posies. What's more, purple berries suddenly appear on the plant.

"Wow!" says Blast. "Is it a new Pellet Posy?"

"Those berries look too round to be pellets," I say. "Can we climb up the stem and get those berries? I wonder what they do." I walk over to the bottom of the plant. Sure enough, I can climb up on it, and Stacy and Blast follow me. We reach the berries in no time. But as soon as we get up there, I get a really bitter taste in my mouth, which nearly makes me gag.

"Ugh!" Blast says. "What is that? It's so... bitter!"

"It's gotta be the berries..." says Stacy. She just barely licks the berry, but her face instantly puckers. Her face just stays like that for a moment. In fact, her entire body doesn't move for a moment. Her prolonged reaction to the berries makes Blast and I laugh, despite the bitterness. After another moment, she glares at us.

"Done yet?" she snaps. We stop laughing immediately. "Anyway, it looks like these berries can paralyze you, so don't lick it," she says.

"Should we bring back a berry and show the rest of the Pikmin? There's gotta be something we can do with these berries," I suggest.

"Sure, why not?" Blast says. "What harm will it do?"

"Besides paralyzing someone, I don't know," Stacy responds. "Well then, let's get one of these berries off...uh...why is it so stuck?"

Oh. I hadn't noticed it till now, but the berries are stuck to the plant by really sticky sap. We have to hit the berry many times before it falls off.

"Ugh, that took forever," I say. "Oh well. Let's bring it back to the landing site." The berry is small enough that it only needs one of us to carry, and Stacy volunteers to carry it. She manages to ignore the bitterness of it as we return to the landing site. Much to our relief, the group is still there, but they're loud as ever. Their disputes really get on my nerves.

"Hey, look what we found!" I shout. The others don't hear me. I can barely even hear myself.

"Ready?" says Blast, nodding at us. "One... two... three..."

"SHUT UP!" we all yell at the same time. Nothing. Still arguing.

"They're too loud for us..." Stacy laments. "Oh well, let's just have the Onion take the berry." She carries the berry over to the Yellow Onion, and the berry is absorbed.

"Uh, you said the berry is paralyzing...?" Blast mentions.

"Oh...oops," Stacy says, realizing her mistake, laughing nervously. "Well, it should be okay." But it ends up not being okay. The Onion doesn't eject a seed, and it starts making a sputtering noise, which is weird. Then the Onion tries taking off to resist the effects of the berry, still sputtering. Then something REALLY weird happens: the entire Onion just stops in midair, and it turns to stone! It crashes to the ground, which captures the attention of the other Pikmin. Their mouths drop as they look at the petrified Onion. Thankfully, the stone crumbles and disappears, and the Onion returns to normal.

"What... What happened?!" shouts one of the Pikmin, looking at us. "What did you do?!"

"Well... We found a weird plant with super bitter berries over by the bomb rocks, and we brought one of the berries back and had the Onion take it..." I explain.

"A plant with bitter berries, huh," the Pikmin says. "At least the Onion is okay. Can you show us the plant?"

"Yeah, sure," I say. "Follow me." We take the shortcut, which involves us going through a small pool. The Blues lifeguard us across and we reach the plant. The other Pikmin just stare at it. Then some Pikmin look really confused, and others look excited.

"What's it called?" asks an inquisitive Red Pikmin. I hadn't thought to give it a name until now, and the question catches me off guard.

"Oh, uh... Hmm... Let's call it—"

"A Bitter Plant!" Blast exclaims, cutting me off. I shoot him a look for interrupting me, but we all agree to the name anyway.

"Hey, where's Splash?" Stacy suddenly asks. I look around and I don't see Splash either.

"Is he studying _again?_ " complains a Blue Pikmin. How typical... Well, the Bitter Plant would certainly fascinate him.

"...I'll go get him," another Blue Pikmin begrudgingly says, and he rushes off to the landing site to get Splash. In the meantime, the Pikmin start talking about the Bitter Plant. I overhear a couple of Pikmin daring one of their friends to go up and eat part of a berry. This can't end well, but the idea of a Pikmin eating part of a berry... Stacy decided to lick the berry, and she was paralyzed, so if he eats part of a berry... Well, he's climbing up the stalk now. He has the same reaction as me when I first got up there. After a moment, he bites one of the berries. To his surprise, a purple liquid gushes out from the hole, covering him in it. He's instantly turned to stone! His friends look horrified as he falls off the Bitter Plant, and I start chuckling. The Pikmin-turned-statue returns to normal after a moment, but he looks angry at one of his friends, and tackles him. I laugh as they wrestle on the ground, and it looks like some other Pikmin are laughing at the scene, too.

I see Splash emerge from the landing site after a few more moments, but it looks like he's complaining to the Pikmin who bringing him here, who is having to drag him by his stem. Jeez, Splash really is skeptical of new things. Even so, it looks like he brought his suitcase full of tools and stuff. Whenever he comes outside, he brings his suitcase in case there's a new discovery. At any rate, as they get closer, I start making sense of his complaints: "...there is no new plant! I am telling you, only Pellet Posies could possibly grow that fast, and what you described didn't sound like a Pellet Posy! Let me go! I demand to be released! My studies are very important, and I will not—"

"Will ya can it Splash and look up there?" the Pikmin says. Splash looks at the Bitter Plant, and is taken aback. "My goodness!" he exclaims, backing away from it to get a full view. "This is... This is _incredible!_ " He immediately runs up to the Bitter Plant and begins examining it. He takes a small knife out of his suitcase and cuts a sliver of the main stalk off, carefully sealing the sample in a bag.

"Could one of you get a berry, too?" he asks.

"Okay," I say. I hastily make my way up the plant and knock off a berry. I let go of the Bitter Plant and fall to the ground. Splash goes over to take a sample from the berry, but Stacy warns him.

"Wait Splash! If you cut into it, purple liquid will come out and turn you into a statue!"

"Nonsense. The way that it fell down implies that it has a solid interior," he says, completely dismissing her warning. Splash has a habit of being stubborn when it comes to new discoveries like this. Guess he'll find out the hard way. He cuts into it, and like Stacy said, the purple liquid bursts out of the berry and turns him into stone. The Pikmin laugh at him, and after a moment, he's released. Normally he would've glared at them or something, but instead he's... _ecstatic._ He's frantically observing the berry, using various tools to observe and analyze it, and writing down notes all the while. I can't blame him though – we haven't had any new discoveries for a while, so he's shut himself up in his lab, doing...uh, well, doing things researchers do, I guess.

Anyway, I see him grab a few samples from the berry. He goes back over to the Bitter Plant and gets a couple more samples from it, too. Then in an instant, he bolts to the landing site, clearly in a hurry to make a full analysis. I've never seen Splash this excited before. Even though we ridicule Splash, he's been pretty important in making helpful tools for us. Curious as to what he'll find out, I also head back to the landing site. Some Pikmin follow me, and eventually the whole group is coming along, too. We return to the landing site, and heavy suspense hangs in the air as we await news from Splash.

* * *

Two hours pass, and no news from Splash. The other Pikmin have gotten into a huge argument over what the berries could be used for, even though it's pretty obvious that all they can do is petrify stuff. Well, there's always going to be that odd bunch that disagrees with stuff, I guess.

Anyway, Splash finally appears and clears his throat, which attracts the attention of all the others. After a moment, he begins to speak: "After rigorous experimentation and careful observation, I've concluded that the ultra bitter essence contained in these berries can be used to turn enemies to stone!"

We're all pleasantly surprised. Some members of the group begin cheering. This should be very useful!

"Hold on, I'm not finished yet," Splash interjects. "I require ten berries in order to create a significantly powerful dosage that's effective against the enemies. The good news is that the berries grow back very quickly after the Bitter Plant is harvested, so we can create many dosages. I've taken the liberty to name this concoction an ultra bitter spray." Ultra bitter spray, huh... Seems fitting, I guess.

"Go harvest some berries and bring them to the Blue Onion," Splash commands.

"Wait! Bringing a berry to the Onion will freeze it!" Stacy points out. This time, Splash takes her seriously, knowing full well the effects of the berries.

"Fine. I'll tell the mechanics to reroute some things in the Onion's Main Processor. Anyway, please go harvest some berries," he finishes. He goes back into the Onion, apparently waiting to convert the berries into a spray. (By the way, the Main Processor is what converts monsters and pellets into energy, which then germinate dormant Pikmin seeds inside the Onion. The rest of the energy is used to power the Onion.)

We return to the site of the Bitter Plant. Since all of us climb up onto the Bitter Plant, we knock the berries off pretty quickly. Five Blue Pikmin grab the berries and take them back to their Onion. We wait around for new berries to appear, and sure enough, after a few more moments, five new berries appear on the plant.

"Wow! They _do_ grow back really fast!" exclaims Blast.

"What, did you not trust Splash?" I say in a sarcastic tone.

"I, no, it's not... It's just... I didn't..." he mumbles, having been surprised by my remark.

"Sure," I say, not buying it. While we were distracted, the rest of the Pikmin had already climbed up the Bitter Plant. One by one, the purple berries fall off the plant, and the Blue Pikmin proceed to take them back. Since we've now gathered the ten berries, the rest of us return to the landing site as well.

Not even a whole minute passes after the last berry is absorbed by the Onion, and once again Splash emerges from it.

"This, my friends, is the ultra bitter spray," he announces, showing us a spray bottle with a purple liquid inside it. We crowd around him to get a look at it. Despite how simple it looks, we're all fascinated by it.

"Oh! Oh!" pipes up a Red Pikmin. "We could use it against the Snagrets!"

Massive approval surges through the crowd. We might stand a chance against the Snagrets this time! We start making the necessary preparations for the battle. All the Blue Pikmin except for Splash return to their Onion, and most of the Yellows return to my Onion, except for my friends and I, and 11 other Yellows. About 100 Red Pikmin come onto the field.

"Alright, Yellows, go get some bomb rocks. We'll meet you up by the two ponds," Splash says, and he goes off, leading the group of Red Pikmin with him.

* * *

We all meet up again after us Yellows went to get bomb rocks. At Splash's request, a single Red Pikmin wanders into Snagret territory to get the Snagrets to notice him. Soon enough, they do, and the Red Pikmin comes running right back. Thank goodness there's only two Snagrets. Fighting three would have been much harder.

"This is where things have to be timed perfectly," Splash says. "I'll run out onto the field and freeze both Snagrets using the ultra bitter spray. Then, the Yellows go in and throw the bomb rocks at them. The explosions should make the Snagrets considerably weaker. After that, we go in and finish them off with the Reds."

We all nod in agreement. Both of the Snagrets retreat underground, having lost sight of their prey. Splash goes onto their plain, and just as quickly as they left, the Snagrets come back, this time close to each other. Splash unleashes the ultra bitter spray on them and the Snagrets turn into stone.

"Bomb them, now!" he demands, while us Yellows trade places with him. We quickly throw seven bomb rocks at each of the Snagrets, and we go back as well. Just before the Snagrets are able to break free of the stone, I hear a deafening explosion as all the bomb rocks go off at once. When they are released, I hear a cry of agony come out of the tyrannical half-bird half-serpents, which return to their subterranean dwelling again.

This is our chance. We all go onto their plain again, and the Snagrets emerge one last time. We throw Red after Red in rapid succession, finishing off both of the helpless Snagrets. They let out a final wail before dying. Usually Snagrets would completely explode, leaving behind nothing but a lot of pellets, but these Snagrets didn't die normally. Instead, only their heads are left behind, along with three 5-pellets from each Snagret. We cheer and celebrate regardless, happy that we're victorious. We begin to carry our spoils back to the landing site. We can barely even carry them because we're all still so excited. These ultra bitter sprays really are going very useful...

However, something terrible happens as we approach the landing site: the ground starts shaking very violently. We're all knocked to the ground, releasing our spoils in the process. We begin to panic, but the ground is shaking so strongly that we can't get back up. As long as any of us have been alive, none of us have ever felt an earthquake. We look up, and see the trees in the background swaying intensely. We hear the cries of the creatures in the forest as they try to flee, and the moans of the wooden tree trunks as they are bent against their normal shape. I see hundreds of birds fly away. Even the Onions have a hard time staying on the ground, and lift off to avoid damage. We panic even more at the thought of being abandoned, but luckily for us, they merely hover in midair.

After a minute, the shaking finally abates, and the ground calms down. The Onions land, we get up, and we look around for any signs of damage. Fortunately, we don't see anything damaged, or changed for that matter. However, we're all on edge by the sudden earthquake, so we hastily take the spoils to the Onions. They produce 15 Reds, 25 Yellows, and 20 Blues, for a grand total of 60 new Pikmin! Still, because we don't know what could happen next, we decide to take off for the day. It's late afternoon anyway...

But before I go into my Onion, I could have sworn I heard a terrifying howl in the distance...

* * *

 **DISCLAIMER: Pikmin and related elements are owned by Nintendo.**

 **Author's Note: Sorry! So sorry! It's been 3 months since I updated... But I hope that the length of this chapter made up for the wait! So does anyone have an idea of what that howl meant? Ah, cliffhangers... I'll try to update more often! No promises, though. Anyway, I hoped you enjoyed this chapter!  
**

 **-PikFan23**


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